This slide deck introduces many, but by no means all, features of Next-Generation clustered Heat Maps (NG-CHMs). For concreteness, it’s based on: A TCGA.

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Presentation on theme: "This slide deck introduces many, but by no means all, features of Next-Generation clustered Heat Maps (NG-CHMs). For concreteness, it’s based on: A TCGA."— Presentation transcript:

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This slide deck introduces many, but by no means all, features of Next-Generation clustered Heat Maps (NG-CHMs). For concreteness, it’s based on: A TCGA mRNA expression (rows) vs. samples (columns) NG-CHM for breast cancer (as part of our TCGA NG-CHM Compendium: The specific map: %2F%2Fbioinformatics.mdanderson.org%2FTCGA%2FNGCHMPortal%3Fview%3D0%26p0DiseaseInput%3Dbrca (too long, sorry) %2F%2Fbioinformatics.mdanderson.org%2FTCGA%2FNGCHMPortal%3Fview%3D0%26p0DiseaseInput%3Dbrca If you have a large monitor or two monitors, you might want to open the breast cancer map in a separate window to explore while you’re going through the tutorial. Each index entry on slide 2 link to the corresponding slide – which links back to slide 2. Note: not all features are pertinent to any given map in the compendium (e.g., a gene- name link-out to GeneCards wouldn’t be pertinent to for a copy number variation map. A more complete, detailed tutorial plus other videos can be found at Tutorial: Navigating Interactive “Next-Generation Clustered Heat Maps” Tutorial: Interactive Next-Generation Clustered Heat Maps

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Covariates that can be added or subtracted Shift-click on map to zoom out Labels show up after repeated zooming in Back to Index Slide

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Covariates that can be added or subtracted To navigate: Drag on map (or click on desired position in Navigator Window) Back to Index Slide

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Covariates that can be added or subtracted Shift-click anywhere on heat map to zoom out Back to Index Slide

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Right-click (PC) or Control-click (Mac) on a row label (gene) to open a Row Label Menu of: statistical analysis windows link-outs for information on the gene Back to Index Slide

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Select “View Box Plot” from Menu Back to Index Slide

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Link-out to an interactive ideogram viewer to show chromosome location(s) of one or more user- selected genes. The viewer has link- outs to other resources, including the UCSC Genome Browser Back to Index Slide

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Covariates that can be added or subtracted Shift-drag to select a region, then right- click (PC) or control-click (Mac) to open the Matrix Menu. Back to Index Slide (Can also select a region by clicking on a branch in one or both dendrograms.)

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Click on map to zoom in Lock horizontal axis to zoom asymmetrically, continuing to show all samples but only a subset of genes Back to Index Slide

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Click on map to zoom in Lock vertical axis to zoom asymmetrically, continuing to show all genes but only a subset of samples Back to Index Slide

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Click on map to zoom in Toggle among CHMs with same cluster tree but different data (e.g., main map and data-point p-values) Back to Index Slide

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Click on map to zoom in Go back / Go forward (i.e., Un-do / Re-do) – especially important unless you never make a mistake Back to Index Slide

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Click on map to zoom in Return to home page Back to Index Slide

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“Views” Pull-down menu: Fit view: Fits entire CHM in the display window Ribbon view: To scan through genes while showing all samples Original view: Back to the original default view of the CHM Back to Index Slide

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“Miscellaneous” menu: PDF: Produces high-resolution PDF (of current state of image) that meets publication standard for all major journals Metadata: Access all metadata necessary to reproduce the NG-CHM months or years later Back to Index Slide

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End of quick tutorial – which doesn’t attempt to cover additional features such as symmetrical NG-CHMs, compound CHMs, methods for zooming based on dendrogram branches, etc. For more detail, seehttp://bioinformatics.mdanderson.org/ main/Navigating_Clustered_Heatmapshttp://bioinformatics.mdanderson.org/ main/Navigating_Clustered_Heatmaps Back to Index Slide